Tumor-wide RNA splicing aberrations generate immunogenic public neoantigens

Abstract

T-cell-mediated immunotherapies are limited by the extent to which cancer-specific antigens are homogenously expressed throughout a tumor. We reasoned that recurrent splicing aberrations in cancer represent a potential source of tumor-wide and public neoantigens, and to test this possibility, we developed a novel pipeline for identifying neojunctions expressed uniformly within a tumor across diverse cancer types. Our analyses revealed multiple neojunctions that recur across patients and either exhibited intratumor heterogeneity or, in some cases, were tumor-wide. We identified CD8+ T-cell clones specific for neoantigens derived from tumor-wide and conserved neojunctions in GNAS and RPL22, respectively. TCR-engineered CD8+ T-cells targeting these mutations conferred neoantigen-specific tumor cell eradication. Furthermore, we revealed that cancer-specific dysregulation in splicing factor expression leads to recurrent neojunction expression. Together, these data reveal that a subset of neojunctions are both intratumorally conserved and public, providing the molecular basis for novel T-cell-based immunotherapies that address intratumoral heterogeneity.

Challenges in the discovery of tumor-specific alternative splicing-derived cell-surface antigens in glioma

“…We should incorporate the lessons learned during this quest as we chart our course. Redirecting our efforts toward intracellular, MHC-presented antigens arising from AS [27] and other tumor-specific post-translational events could offer a more viable avenue. This path may offer more attainable prospects within the expansive landscape of cancer immunotherapy.…”

“…In this study, we investigated tumor-specific AS events in glioma as a potential source of untapped neoantigens, with a particular focus on putative cell-surface antigen candidates derived from these events. Importantly, because major histocompatibility complex (MHC)-epitope-type neoantigens have been studied using different analytical approaches and reported separately [26,27], our investigation exclusively focused on the AS events occurring at the cell-surface that are independent of MHC presentation. These cell-surface candidates could serve as targets for antibodies and CAR-T cells in future therapeutic development.…”